The intra-basin variability of snowmelt and melt-water runoff hydrology in an 8 km2 subarctic alpine tundra catchment was examined for the 2003 melt period. The catchment, Granger Creek, is within the Wolf Creek Research Basin, Yukon, which is typical of mountain subarctic landscapes in northwestern Canada. The study catchment was segmented into nine internally uniform zones termed hydrological response units (HRUs) based on their similar hydrological, physiographic, vegetation and soil properties. Snow accumulation exhibited significant variability among the HRUs, with greatest snow water equivalent in areas of tall shrub vegetation. Melt began first on southerly exposures and at lower elevations, yet average melt rates for the study period varied little among HRUs with the exception of those with steep aspects. In HRUs with capping organic soils, melt water first infiltrated this surface horizon, satisfying its storage capacity, and then percolated into the frozen mineral substrate. Infiltration and percolation into frozen mineral soils was restricted where melt occurred rapidly and organic soils were thin; in this case, melt-water delivery rates exceeded the frozen mineral soil infiltration rate, resulting in high runoff rates. In contrast, where there were slower melt rates and thick organic soils, infiltration was unlimited and runoff was suppressed. The snow water equivalent had a large impact on runoff volume, as soil storage capacity was quickly surpassed in areas of deep snow, diverting the bulk of melt water laterally to the drainage network. A spatially distributed water balance indicated that the snowmelt freshet was primarily controlled by areas with tall shrub vegetation that accumulate large quantities of snow and by alpine areas with no capping organic soils. The intra-basin water balance variability has important implications for modelling freshet in hydrological models. Copyright © 2006 John Wiley & Sons, Ltd.